Gene Expression Chapter Eleven

What is Gene Expression? When a gene is expressed – that gene’s protein product is made: 1.DNA is transcribed into RNA 2.RNA is translated into Protein 3.Protein is folded and transported so it is functional When a gene is not expressed – these steps do not happen Gene is “silenced” – function is off

What is Gene Expression? We all have the same genes: –Different races –Apes and Humans –Fruit Flies and Humans –Different cell types – bone vs. eyeballs So what makes us so different? It’s not what genes we are carrying It’s how and when those genes are expressed

Questions to ask… 1.How does a bone cell know to express the proteins that make it a bone, and not an eyeball? 2.How do blood stem cells know when to become red blood cells, white blood cells or platelets? 3.What makes us human and them apes? What regulates gene expression?

How is expression regulated? Transcription Factors – bind specifically to gene’s promoters – turn on and off Methylation – silencing of huge sections of DNA Acelylation – activating huge sections of DNA Chromatin and histones – bound will cause a gene to be silenced

How is expression regulated? RNAi – small pieces of RNA bind to mRNA and effectively remove it before it can be translated into protein Exon shuffling – one gene encodes for different proteins – depends on which exons translation machinery “keeps” Protein folding – one protein can be folded differently to have different functions – depends on enzymes and chaperones

How is expression regulated? All levels of transcription and translation are involved: 1.DNA sequence will encode for specific regulation – promoters, exons/introns, etc 2.RNAs – will affect which genes complete the process to become proteins 3.Proteins – function as enzymes and machinery to activate or silence specific genes

Transcription Factors Proteins that bind: –Promoters –Enhancers or Repressors Initiate transcription by bringing over RNA Polymerase and other proteins to the start site of transcription Or repress transcription by blocking proteins from binding at start site

Methylation and Acetylation Methylation adds -CH 3 Acetylation adds-CO 2 CH 3 Methylation causes DNA to be silenced: –Heterochromatin (darker stained regions of chromosomes) –Example = Imprinting Acetylation causes DNA to be activated: –Move histones away from transcription start site

Histones Histones are proteins that wrap up DNA in order to condense it into Nucleus When Histones are binding DNA ? DNA is silenced: –RNA Polymerase can’t bind When Histones come off DNA ? DNA is free to be expressed: –RNA Polymerase can bind – transcription

RNAi Sometimes small interfering RNAs are made –siRNA They will bind to mRNA –Based on complementary base pairing mRNA and siRNA complex will be destroyed Therefore mRNA cannot be translated into protein

Exon Shuffling One gene can choose different exons and skip past others Therefore one gene can make many different proteins The transcription and translation machinery will regulate which exons to are used and which are skipped Depending on tissue and developmental time point – different proteins made

Exon Shuffling

Alternative Splicing Many mRNA sequences can be spliced differently Thereby producing more than one protein from same sequence AB C D E Promoter A B C E A C D E

Protein Folding Sometimes protein sequence can fold in more than one way Sequence Structure 1 Function A Structure 2 Function B

Protein Folding One protein sequence can be folded in more than one way Depends on: –Enzymes –Chaperone proteins Different enzymes will be present in different tissues or at different developmental time points – therefore forming different proteins depending

How is expression regulated? 1.Transcription Factors 2.Methylation 3.Acelylation 4.Chromatin and histones 5.RNAi 6.Exon shuffling 7.Alternative Splicing 8.Protein folding

Hemoglobin Subunits Excellent example of gene expression regulation Hemoglobin is a protein Made of four subunits Each subunit carries a “heme” group –Transports Oxygen –Bound to Iron

Hemoglobin Subunits During development mammals receive oxygen from different sources: 1.Embryonic – oxygen comes directly from mother’s tissues 2.Fetal – oxygen comes through placenta 3.Adult – oxygen comes through lungs Hemoglobin subunits change according to developmental time point to handle this

Hemoglobin Subunits Hemoglobin subunits: 1.Embryonic – 2 epsilon and 2 zeta subunits 2.Fetal – 2 alpha and 2 gamma subunits 3.Adult – 2 alpha and 2 beta subunits “Locus Control Region” produce proteins that oversee the assembly of hemoglobin and which subunits are used

Blood Cell Types In bone marrow – one pluripotent stem cell –Can make different types of cells Has to choose between becoming: –Red Blood Cell Filled with hemoglobin –White Blood Cell Protecting the body from infection –Platelets Blood clotting

Blood Cell Types Actually this is more accurate:

Blood Cell Types Bone Marrow – pluripotent stem cell Choice based on gene expression: –Red Blood Cell Bone marrow activates pathway 1 –White Blood Cell Pathway 2 –Platelets Pathway 3 Think about disease or sickness

Bone vs. Eyeball? Developing organs depends on: –Differential gene expression –At specific developmental time points

Bone vs. Eyeball? 1.Transcription Factors 2.Methylation 3.Acelylation 4.Histones 5.RNAi 6.Exon shuffling 7.Alternative Splicing 8.Protein folding All of these levels of control are happening Each controlled by: Developmental time points Differences in tissue types Differences in genetic sequence

Proteomics Study of the structure and function of proteins, including the way they work and interact with each other inside cell Also - analysis of the protein complement of the genome Or in other words, which proteins are expressed And at what level?

Example from Proteomics

One Gene – Many Proteins 1.Exon Shuffling 2.Protein Folding 3.Genes in both directions –Another gene lies hidden in the opposite direction –When DNA is read 5’ to 3’ (non-coding strand) will form a second protein 4.Genes within introns –A second gene is hidden inside the introns of first

What else is in the Genome? Only 1.5 % of genome is actually encoding genes What is the other 98.5 % then? –Regulation sequences: promoters, enhancers, repressors, etc –Noncoding RNA – tRNA, rRNA, etc –Introns – regulation? other genes? –Repeats – unknown function (Some believe repeats are leftovers from evolution)

What else is in the Genome? Genes Regulation Introns Non-coding RNA Repeats

Summary Gene expression – is when a gene is transcribed and translated into a functional protein Regulation of expression happens at: –DNA, RNA and protein level Learn 8 different methods to regulate gene expression and be able to tell them apart Know how one gene can lead to many proteins

Next Class: Read Chapter Twelve Homework – Chapter Eleven Problems; –Review: 1,3,4,7,13,15 –Applied: 3,4,6,8